As a means for detecting a target substance such as DNA, proteins, or the like, commonly used is a method in which a target substance is labeled with fluorescence, irradiated with a predetermined excitation light such as laser, or the like, and the fluorescence thus emitted is detected. As an application of the method, a parallel sequencer, wherein DNA or RNA is immobilized on a substrate to determine the nucleotide sequence thereof, has been proposed. At present, commercially available parallel sequencers have dramatically improved the number of nucleotide read and the number of parallel per analysis by arranging a large number of DNA fragments to be read. Most of the parallel sequencers read a nucleotide sequence targeting clusters of copied DNA strands. However, the cluster formation not only requires time and the cost of a reagent but a phenomenon (dephasing) in which the sequence reaction loses the synchronicity between the DNA strands also occurs and hence limits the read length. Further, it is not suitable for quantitative analysis because the deviation is caused between the DNAs easy to be amplified and hard to be amplified. Thus, as a system for solving these drawbacks, a single molecule DNA sequencing method has been proposed. In this system, the nucleotide sequence for every single DNA molecule can be determined which thus eliminates the need for the purification and amplification of a sample DNA in cloning, PCR, or the like, that have been the problem in the conventional art, and hence faster genome analysis and gene diagnosis can be expected. One of such systems is SMRT technology of Pacific Biosciences Inc. (see Non-Patent Literature 1). In the SMART technology, a substrate in which a large number of several tens-nm holes called zero-mode waveguidances (ZMW) are aligned is produced and a single molecule of polymerase is placed in each of the holes. Nucleotides labeled with fluorescent dyes are incorporated therein and the fluorescence detection is carried out while the nucleotides are allowed to elongate to obtain the sequence information of each fragment. Such a technique wherein the detection is carried out while allowing the elongation with the incorporation of nucleotides is usually called Sequencing by synthesis. However, when the ZMW is used, the single molecule placement of a polymerase depends on the probability and consequently holes in which a single polymerase molecule is placed account for theoretically up to about 30% out of a large number of holes produced. In Sequencing by synthesis, a continuous nucleotide elongation reaction is detected and thus the field of vision to be detected cannot be moved until one cycle of elongation reaction is completed. Accordingly, to measure many samples at one time, it is desirable to immobilize samples as high density as possible, which is a factor to determine the final sequencing performance.
Various techniques have been reported for immobilizing on an analysis device a plurality of chemical substances such as nucleic acid, or the like, including DNA (see Patent Literatures 1 and 2).